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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
NeuroMorpho.OrgResource, service resource, data or information resource, data repository, storage service resource, databaseCentrally curated inventory of digitally reconstructed neurons associated with peer-reviewed publications that contains some of the most complete axonal arborizations digitally available in the community. Each neuron is represented by a unique identifier, general information (metadata), the original and standardized ASCII files of the digital morphological reconstruction, and a set of morphometric features. It contains contributions from over 100 laboratories worldwide and is continuously updated as new morphological reconstructions are collected, published, and shared. Users may browse by species, brain region, cell type or lab name. Users can also download morphological reconstructions for research and analysis. Deposition and distribution of reconstruction files ultimately prevents data loss. Centralized curation and annotation aims at minimizing the effort required by data owners while ensuring a unified format. It also provides a one-stop entry point for all available reconstructions, thus maximizing data visibility and impact.neuron, morphological reconstruction, morphometry, axonal arborization, digital neuronal reconstruction, neuronal reconstruction, neuronal morphology, data sharing, annotation, brain region, neocortex, digital reconstruction, neurogenetics, neurochemistry, neuroscience, neurologySCR_002145(NeuroMorpho.Org, RRID:SCR_002145)George Mason University; Virginia; USA MURI, NINDSrelated to: DONE: Detection of Outlier NEurons, NIF Literature, Computational Neurobiology and Imaging Center, Integrated Manually Extracted Annotation, used by: NIF Data Federation, recommended by: National Library of Medicine, BRAIN Initiative, listed by:, NeuroImaging Tools and Resources Collaboratory (NITRC)References (3)Last checked downnif-0000-00006
flytrapResource, image, data or information resource, video resource, databaseFlytrap is an interactive database for displaying gene expression patterns, in particular P(GAL4) patterns, via an intuitive WWW based interface. This development consists of two components, the first being the HTML interface to the database and the second, a tool-kit for constructing and maintaining the database. The browser component of the project is entirely platform independent; based on javascript and HTML and therefore only requires a "standard" browser. This is to facilitate CD-ROM distribution and off-line browsing. Whether on-line or on CD, the basic browser structure does not reply on any server based scripts. Basic searching is now available. The search page uses javascript and will work off-line (i.e. from a CD-ROM copy). The construction tool-kit is UNIX based and requires an on-line web server. The tool-kit is used to compile the HTML browser interface from a simple database. The tool-kit part comprises a forms based HTML interface to the datasets allowing new information to b e added and updated very simply. We are also developing a java interface for the tool-kit that will enable us to edit and annotate images on-line. The basic browser interface is complete and a demonstration version can be accessed via the website. The first working version of the tool-kit is now on-line and is available for use.brain, genetics, 3d model, expression pattern, anatomy, anatomical structure, cell, gene expression, brain function, neuroimagingSCR_003075(flytrap, RRID:SCR_003075)University of Edinburgh; Scotland; United Kingdom BBSRC, EPSRCLast checked upnif-0000-00051
NeuronBankResource, wiki, narrative resource, database, data or information resourceWiki for Neuroscientists to describe neurons and neural circuitry. Registered users may edit. The ultimate goal is advance the field of Neuromics by creating an encyclopedia of neurons and neural circuitry. NOTE: The database is no longer being maintained due to lack of funding. All of the information about the neurons is available on the NeuronBank Wiki. NeuronBank organizes information about identified neuron location, physiology, morphology, and connectivity, and helps researchers to browse through known circuits, conduct comparative work between species, and classify new cell types. The NeuronBank BranchKB produces a web-based knowledge management system that can be easily customized to handle information about any type of nervous system. NeuronBank will serve as a repository for new observations of identified neurons and their synaptic connections. Importantly, new observations will be uniquely citable and credited to the reporting lab. NeuronBank Central will provide searches across published species databases. This federated knowledge-management system pushes forward several innovative computer science technologies and will serve an important need in the neuroscience community. Nervous systems from different species will be represented in different branches. Users can search within one branch or search across branches for features of neurons and neural circuits.invertebrate, tritonia, melibe, neurome, neuron, neural circuit, synaptic connectivity, connection, wiring diagram, nervous system, catalogSCR_005058(NeuronBank, RRID:SCR_005058)Georgia State University; Georgia; USA Georgia State University; Georgia; USA, Human Brain Project, NIMH, NINDS, NSFLast checked upnif-0000-00238
Universal Protein ResourceResource, database, portal, data or information resourceCollection of data of protein sequence and functional information. UniProt databases are UniProt Knowledgebase (UniProtKB), UniProt Reference Clusters (UniRef), and UniProt Archive (UniParc).collection, protein, sequence, annotation, data, functional, informationSCR_002380(Universal Protein Resource, RRID:SCR_002380) PIR , European Bioinformatics Institute , SIB Swiss Institute of Bioinformatics British Heart Foundation, NCRR, NHGRI, NIGMS, NLM, NSFrelated to: ClustalW2, UniProt DAS, UniParc at the EBI, ProDom, LegumeIP, Pathway Commons, NIH Data Sharing Repositories, FlyMine, IMEx - The International Molecular Exchange Consortium, 3D-Interologs, Biomine, EBIMed, STOP, Coremine Medical, BioExtract, STRAP, GOTaxExplorer, GoAnnotator, IT-GOM: Integrated Tool for IC-based GO Semantic Similarity Measures, Whatizit, MOPED - Model Organism Protein Expression Database , Polbase, PredictSNP, PSICQUIC Registry, IntAct, p300db, used by: LIPID MAPS Proteome Database, ChannelPedia, Open PHACTS, DisGeNET, Smart Dictionary Lookup, MitoMiner, Cytokine Registry, MobiDB, Pathway Analysis Tool for Integration and Knowledge Acquisition, Phospho.ELM, GEROprotectors, listed by:, LabWorm, works_with: Genotate, CellPhoneDBReferences (7)Last checked upnif-0000-00377
GeneNetworkResource, service resource, data or information resource, data repository, storage service resource, databaseCollection of data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. Sequence data (SNPs) and transcriptome data sets (expression genetic or eQTL data sets). Quantitative trait locus (QTL) mapping module that is built into GN is optimized for fast on-line analysis of traits that are controlled by combinations of gene variants and environmental factors. Used to study humans, mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley and Arabidopsis). Users are welcome to enter their own private data.gene, genetic correlation, genome, abi panther, genome browser, genomic region, genotype, gnf expression atlas, mouse, network, phenotype, relational database, sequence, snp, trait, transcriptome, transcript, webgestalt, molecular neuroanatomy resource, source code, toxicity, cancer susceptibility, behavior, allelic variant, environmental factor, mrna, expression, microarray, annotation, data analysis service, mapping, quantitative trait locus, phenotype, data sharingSCR_002388(GeneNetwork, RRID:SCR_002388)University of Tennessee Health Science Center; Tennessee; USA NCI, NCRR, NIA, NIAAA, NIDA, NIGMSrelated to: Monarch Initiative, NIH Data Sharing Repositories, used by: NIF Data FederationReferences (2)Last checked upnif-0000-00380
FlyBaseResource, topical portal, organism-related portal, analysis service resource, database, data analysis service, service resource, portal, production service resource, storage service resource, data repository, data or information resourceDatabase of Drosophila genetic and genomic information with information about stock collections and fly genetic tools. Gene Ontology (GO) terms are used to describe three attributes of wild-type gene products: their molecular function, the biological processes in which they play a role, and their subcellular location. Additionally, FlyBase accepts data submissions. FlyBase can be searched for genes, alleles, aberrations and other genetic objects, phenotypes, sequences, stocks, images and movies, controlled terms, and Drosophila researchers using the tools available from the "Tools" drop-down menu in the Navigation bar.mutant, gene, genome, blast, genotype, phenotype, allele, sequence, stock, image, movie, controlled term, video resource, image collection, life-cycle, genome, expression, rna-seq, genetics, drosophilidaeSCR_006549(FlyBase, RRID:SCR_006549) University of Cambridge; Cambridge; United Kingdom , University of New Mexico; New Mexico; USA , Harvard University; Cambridge; United States , Indiana University; Indiana; USA Indiana Genomics Initiative, Indiana University; Indiana; USA, MRC, NIH Blueprint for Neuroscience Research, NIHGRI, NSFrelated to: FlyMine, Virtual Fly Brain, AmiGO, Drosophila melanogaster Exon Database, HomoloGene, UniParc at the EBI, UniParc, Gene Ontology, NIH Data Sharing Repositories, GBrowse, Integrated Manually Extracted Annotation, PhenoGO, used by: NIF Data Federation, Resource Identification Portal, Monarch Initiative, PhenoGO, Integrated Animals, Drososhare, listed by:, OMICtoolsReferences (18)Last checked upnif-0000-00558, OMICS_01649
DroID - Drosophila Interactions DatabaseResource, data or information resource, databaseA gene and protein interactions database designed specifically for the model organism Drosophila including protein-protein, transcription factor-gene, microRNA-gene, and genetic interactions. For advanced searches and dynamic graphing capabilities the IM Browser and a DroID Cytoscape plugin are available.interaction, gene, protein, protein interaction, annotation, transcription factor, rna, protein-protein interaction, interactome, gene expression, phenotype, interolog, orthologSCR_006634(DroID - Drosophila Interactions Database, RRID:SCR_006634)Wayne State University School of Medicine; Michigan; USA related to: Cytoscape, listed by: OMICtoolsReferences (2)Last checked upnif-0000-02767, OMICS_01908
Drosophila polymorphism databaseResource, data or information resource, databaseDatabase providing a collection of all the existing polymorphic sequences in the Drosophila genus. It allows users to search for any polymorphic set according to different parameter values of nucleotide diversity. For data collection, diversity measures and updating they use PDA, a pipeline made of a set of Perl modules that automates the process of sequence retrieving, grouping, aligning and estimating diversity parameters from GenBank sequences. Diversity measures, including polymorphism estimates in synonymous and non-synonymous sites, linkage disequilibrium and codon bias, are calculated for each polymorphic set in different functional regions. The database also includes the primary information retrieved from different external sources: the Drosophila publicly available nucleotide sequences (excluding ESTs, STSs, GSSs, working draft and patents) with their annotations and references from GenBank (see the NCBI's Disclaimer and Copyright), additional information of genes and aberrations (from FlyBase), and the cross-references to the PopSet database (from NCBI). The database content is updated daily and records are assigned unique and permanent DPDB identification numbers to facilitate cross-database referencing.polymorphismSCR_007629(Drosophila polymorphism database, RRID:SCR_007629)Autonomous University of Barcelona; Barcelona; Spain Last checked upnif-0000-02769
ESTHERResource, data or information resource, databaseDatabase and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila.alpha hydrolase, beta hydrolase, cholinesterase, protein, protein superfamily, blast, gene, protein binding, protein-protein interaction, nucleotide, nucleotide sequence, enzyme, genetics, genome, genomics, mutation, disease, gene expression, peptide, chromosomeSCR_002621(ESTHER, RRID:SCR_002621)INRA - French National Institute for Agricultural Research; Paris; France related to: UniProtKB, AceDB, listed by: re3data.orgPMID:23193256Last checked upnif-0000-02817, nif-0000-30526, SCR_008479
FlyMineResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceAn integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java APIanopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publicationSCR_002694(FlyMine, RRID:SCR_002694)University of Cambridge; Cambridge; United Kingdom NHGRI, Wellcome Trustrelated to: FlyBase, Universal Protein Resource, Ensembl, InterPro, BioGRID, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Tree families database, IntAct, Gene Ontology, GOA, ArrayExpress, REDfly Regulatory Element Database for Drosophilia, KEGG, ReactomePMID:17615057Last checked upnif-0000-02845
Berkeley Drosophila Genome ProjectResource, topical portal, production service resource, analysis service resource, database, data analysis service, narrative resource, experimental protocol, portal, service resource, material resource, data or information resourceDatabase on the sequence of the euchromatic genome of Drosophila melanogaster In addition to genomic sequencing, the BDGP is 1) producing gene disruptions using P element-mediated mutagenesis on a scale unprecedented in metazoans; 2) characterizing the sequence and expression of cDNAs; and 3) developing informatics tools that support the experimental process, identify features of DNA sequence, and allow us to present up-to-date information about the annotated sequence to the research community. Resources * Universal Proteomics Resource: Search for clones for expression and tissue culture * Materials: Request genomic or cDNA clones, library filters or fly stocks * Download Sequence data sets and annotations in fasta or xml format by http or ftp * Publications: Browse or download BDGP papers * Methods: BDGP laboratory protocols and vector maps * Analysis Tools: Search sequences for CRMs, promoters, splice sites, and gene predictions * Apollo: Genome annotation viewer and editor September 15, 2009 Illumina RNA-Seq data from 30 developmental time points of D. melanogaster has been submitted to the Short Read Archive at NCBI as part of the modENCODE project. The data set currently contains 2.2 billion single-end and paired reads and over 201 billion base pairs.drosophila genome, cdna, est, transposon insertions, genomic sequencing, geneSCR_013094(Berkeley Drosophila Genome Project, RRID:SCR_013094)University of California; Berkeley; USA NHGRI, NIGMSrelated to: Bgee: a dataBase for Gene Expression Evolution, OpenFlyData.orgPMID:21177961Last checked upnif-0000-02867
REDfly Regulatory Element Database for DrosophiliaResource, service resource, data or information resource, data repository, storage service resource, databaseCurated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). Includes experimentally verified fly regulatory elements along with their DNA sequence, associated genes, and expression patterns they direct. Submission of experimentally verified cis-regulatory elements that are not included in REDfly database are welcome.transcriptional cis-regulatory module, transcription factor binding site, dna sequence, gene, expression pattern, genome, gene expression, transcription factor, cis-regulatory moduleSCR_006790(REDfly Regulatory Element Database for Drosophilia, RRID:SCR_006790)University at Buffalo; New York; USA NSFrelated to: Drosophila anatomy and development ontologies, FlyMine, listed by: OMICtoolsReferences (3)Last checked upnif-0000-03393, OMICS_01870
Unified Human InteractomeResource, data or information resource, databaseA database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks.molecular interaction network, interactome, protein, protein interaction network, protein interaction, pathway, function, visualization, protein-protein interaction, transcriptional regulatory interaction, networkSCR_005805(Unified Human Interactome, RRID:SCR_005805)University of Algarve; Faro; Portugal listed by: OMICtoolsReferences (4)Last checked upnif-0000-03609, OMICS_01911
GemmaResource, data or information resource, databaseResource for reuse, sharing and meta-analysis of expression profiling data. Database and set of tools for meta analysis, reuse and sharing of genomics data. Targeted at analysis of gene expression profiles. Users can search, access and visualize coexpression and differential expression results.chip, microarray, functional genomics, gene expression, coexpression, differential expressionSCR_008007(Gemma, RRID:SCR_008007)University of British Columbia; British Columbia; Canada Canadian Foundation for Innovation, Canadian Institutes for Health Research, Michael Smith Foundation for Health Research, NIGMSrelated to: Gene Ontology, Gene Expression Omnibus, Monarch Initiative, Phenocarta, used by: NIF Data Federation, Integrated Data AnnotationPMID:22782548Last checked upnif-0000-08127
Cold Spring Harbor Protocols: Collected Resources - Behavioral AssaysResource, bibliography, data or information resourceA bibliography of published Behavioral Assays by Cold Spring Harbor Protocols. Cold Spring Harbor Protocols is an interdisciplinary journal providing a definitive source of research methods in cell, developmental and molecular biology, genetics, bioinformatics, protein science, computational biology, immunology, neuroscience and imaging. Each monthly issue details multiple essential methods - a mix of cutting-edge and well-established techniques. Newly commissioned protocols and unsolicited submissions are supplemented with articles based on Cold Spring Harbor Laboratorys renowned courses and manuals. All protocols are up-to-date and presented in a consistent, easy-to-follow format.genetics, bioinformatics, cell, computational biology, development, imaging, immunology, journal, molecular, neuroscience, protein, research, behavioral assay, behavior, ant, honeybee, learning, courtship, larvae, adult, stress, olfactory, aggression, sleep, movement, locomotor, circadian, feedingSCR_001697(Cold Spring Harbor Protocols: Collected Resources - Behavioral Assays, RRID:SCR_001697)Cold Spring Harbor Laboratory Last checked upnif-0000-10198
Flybrain at StanfordResource, image analysis software, data processing software, software application, image collection, software resource, data or information resourceProject content including raw image data, neuronal tracings, image registration tools and analysis scripts covering three manuscripts: Comprehensive Maps of DrosophilaHigher Olfactory Centres : Spatially Segregated Fruit and Pheromone Representation which uses single cell labeling and image registration to describe the organization of the higher olfactory centers of Drosophila; Diversity and wiring variability of olfactory local interneurons in the Drosophila antennal lobe which uses single cell labeling to describe the organization of the antennal lobe local interneurons; and Sexual Dimorphism in the Fly Brain which uses clonal analysis and image registration to identify a large number of sex differences in the brain and VNC of Drosophila. Data * Raw Data of Reference Brain (pic, amira) (both seed and average) * Label field of LH and MB calyx and surfaces for these structures * Label field of neuropil of Reference Brain * Traces (before and after registration). Neurolucida, SWC and AmiraMesh lineset. * MB and LH Density Data for different classes of neuron. In R format and as separate amira files. * Registration files for all brains used in the study * MBLH confocal images for all brains actually used in the study (Biorad pic format) * Sample confocal images for antennal lobe of every PN class * Confocal stacks of GABA stained ventral PNs Programs * ImageJ plugins (Biorad reader /writer/Amira reader/writer/IGS raw Reader) * Binary of registration, warp and gregxform (macosx only, others on request) * Simple GUI for registration tools (macosx only at present) * R analysis/visualization functions * Amira Script to show examples of neuronal classes The website is a collaboration between the labs of Greg Jefferis and Liqun Luo and has been built by Chris Potter and Greg Jefferis. The core Image Registration tools were created by Torsten Rohlfing and Calvin Maurer.brain, cell, neuron, neuropil, olfactory, pheromone, confocal image, antennal lobe, axon trace, forum, neuronal tracing, image registration tool, analysis script, single-cell labeling, image registration, mushroom body, lateral horn, olfactory receptor neuronSCR_001877(Flybrain at Stanford, RRID:SCR_001877)Stanford University; Stanford; California Damon Runyon Cancer Research Foundation, NIAAA, NIDCD, Wellcome TrustPMID:17382886Last checked downnif-0000-10437
Protein LoungeResource, data analysis service, database, analysis service resource, production service resource, narrative resource, service resource, training material, data or information resourceComplete siRNA target database, complete Peptide-Antigen target database and a Kinase-Phosphatase database. They have also developed the largest database of illustrated signal transduction pathways, which are interconnected to their extensive protein database and online gene / protein analysis tools. The interactive web-based databases and software help life-scientists understand the complexity of systems biology. Systems biology efforts focus on understanding cellular networks, protein interactions involved in cell signaling, mechanisms of cell survival and apoptosis leading to development or identification of drug candidates against a variety of diseases. In the post-genomic era, one of the major concerns for life-science researchers is the organization of gene / protein data. Protein Lounge has met this concern by organizing all necessary data about genes / proteins into one portal.gene, antigen, bioinformatics, kinase, life science, peptide, phosphatase, signal transduction pathway, sirna, systems biology, protein, biology, cellular network, protein interaction, cell signaling, cell survival, apoptosis, peptide-antigen, kinase-phosphatase, image, pathwaySCR_002117(Protein Lounge, RRID:SCR_002117)Last checked upnif-0000-20903
GenevestigatorResource, data analysis service, commercial organization, database, analysis service resource, production service resource, service resource, data or information resourceA high performance search engine for gene expression that integrates thousands of manually curated public microarray and RNAseq experiments and nicely visualizes gene expression across different biological contexts (diseases, drugs, tissues, cancers, genotypes, etc.). There are two basic analysis approaches: # for a gene of interest, identify which conditions affect its expression. # for condition(s) of interest, identify which genes are specifically expressed in this/these conditions. Genevestigator builds on the deep integration of data, both at the level of data normalization and on the level of sample annotations. This deep integration allows scientists to ask new types of questions that cannot be addressed using conventional tools.gene, genetic, animal, development, disease, meta-analysis, regulation, stage, microarray, rnaseq, visualization, gene expression, disease, drug, tissue, cancer, genotype, pharma, biomedical, conditions, genotype, anatomy, neoplasm, chemical, hormone, infection, model organism, organ, cell type, cell line, target, biomarker, similaritySCR_002358(Genevestigator, RRID:SCR_002358)Last checked upnif-0000-21172, nif-0000-21172, OMICS_00763
Patterns of Gene Expression in Drosophila EmbryogenesisResource, software resource, source code, database, image collection, data or information resourceDatabase of embryonic expression patterns using a high throughput RNA in situ hybridization of the protein-coding genes identified in the Drosophila melanogaster genome with images and controlled vocabulary annotations. At the end of production pipeline gene expression patterns are documented by taking a large number of digital images of individual embryos. The quality and identity of the captured image data are verified by independently derived microarray time-course analysis of gene expression using Affymetrix GeneChip technology. Gene expression patterns are annotated with controlled vocabulary for developmental anatomy of Drosophila embryogenesis. Image, microarray and annotation data are stored in a modified version of Gene Ontology database and the entire dataset is available on the web in browsable and searchable form or MySQL dump can be downloaded. So far, they have examined expression of 7507 genes and documented them with 111184 digital photographs.embryo, embryogenesis, gene, anatomy, microarray, pattern, protocol, rna, gene expression, expression pattern, embryonic drosophila, in situ hybridization, annotation, estSCR_002868(Patterns of Gene Expression in Drosophila Embryogenesis, RRID:SCR_002868)Berkeley Drosophila Genome Project Howard Hughes Medical Institute, NHGRI, NIGMS, NIHrelated to: Gene OntologyReferences (2)Last checked upnif-0000-25550
Assembly/Alignment/Annotation of 12 Related Drosophila SpeciesResource, data set, topical portal, data or information resource, portal, organism-related portalA single source for sequences, assemblies, annotations and analyses of the genomes of members of the fruitfly genus Drosophlia. It is meant as resource for Drosophilists and other researchers interested in comparative analysis of these species and their genomes. There are pages for each species, as well as pages for different types of multi-species resources (e.g. alignments). If you have a public resource that will help this project, please consider making it available through this page by emailing, annotation, analysis, genome, fruitfly, drosophila, research, comparative, alignment, assemblySCR_002921(Assembly/Alignment/Annotation of 12 Related Drosophila Species, RRID:SCR_002921)Lawrence Berkeley National Laboratory Last checked downnif-0000-30021
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